SeqAfrica: empowering Africa’s fight against antimicrobial resistance through genomics

The ongoing threat of antimicrobial resistance (AMR) demands capacity strengthening in Africa for improved pathogen surveillance. The high-resolution picture of AMR provided by pathogen whole genome sequencing (WGS) can help close data gaps and inform disease prevention strategies, interventions and public health actions. Here, we report on phase 1 of the Fleming Fund-supported SeqAfrica project (2019-2023), one of the first genomic AMR surveillance networks in Africa. SeqAfrica established five regional sequencing hubs across West, East, and Southern Africa, expanded infrastructure, and delivered hybrid training programs to strengthen workforce capacity. During phase 1, the network generated 29,269 pathogen genomes (18,264 bacterial, 300 fungal, and 10,705 SARS-CoV-2) from 21 African countries, contributing to 40 scientific publications and substantial genomic data for national and global surveillance efforts, supporting outbreak investigations and antimicrobial stewardship initiatives. The median turnaround time from sample receipt to data release was 12 weeks (range: 3-104 weeks), demonstrating the feasibility of genomic AMR surveillance despite logistical challenges. By nurturing a community of practice, expanding the workforce, and translating data into actionable insights, SeqAfrica has advanced the integration of pathogen genomics into national and regional surveillance frameworks. However, sustaining this capacity remains a challenge amid global funding constraints, procurement bottlenecks, and workforce retention issues. Lessons learned from implementation include successes in regional collaboration and persistent challenges in procurement, workforce retention, and metadata completeness, which informed the design of phase 2. As Africa continues to invest in genomic health infrastructure, SeqAfrica provides a proven model for embedding pathogen genomics into public health strategies and strengthening AMR surveillance across the continent.